Meltwater ponds are important biodiversity elements in continental Antarctica. Many occupy closed basins and are vulnerable to changes in the balance between water accrual, through melting of ice and snow, and water loss by ablation and evaporation. We use a two-decade long record of ponds on the McMurdo Ice Shelf to assess temporal variability in key limnological variables. Ponds underwent many-fold change in biologically conservative variables, such as conductivity, and changes were similar in ponds from different catchments but of comparable area. In contrast, biologically active variables (pH, inorganic nutrients and planktonic/benthic biomass) are buffered by in-pond processes and show consistency between years and no coherence across catchments. Coherent behaviour across catchments implies an overarching, climatic effect. However, we could identify no signature of summer air temperature or irradiance in pond dynamics, although winter snow deposition may leave a legacy of low conductivity to the following summer. While ponds are clearly affected by climate, our data show that ecosystem responses are complex and highlight the need for system-appropriate, long-term observation if directional environmental change is to be separated from inherent variability in systems that respond to multiple climatic variables and which have significant biological buffering capacity.